M3_Script.Rmd

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#<span style="color:cadetblue">Writing a script</span>

***

This module will cover: 

  - script best practices
  
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

#<span style="color:cadetblue">The importance of a script</span>
>1. Permanent 
>2. Repeatable
>3. Annotated 
>4. Shareable

###<span style="color:orangered">Practice:</span> We will do this exercise together...

##<span style="color:cadetblue">Step 1</span>

```
File --> New File --> R Script or Top left green and white plus sign drop down then select R Script
```

##<span style="color:cadetblue">Step 2</span>

``` 
The # symbols declares that anything after it is a comment

You should start with some information at the top, for example:
#############################
## Author:                ###
## Date:                  ###
## Purpose:               ###
#############################
```

##<span style="color:cadetblue">Step 3</span>

Leave an empty "blank line" - These are important  to create chunks of code and annotation

##<span style="color:cadetblue">Step 4</span>


Next <span style="color:orangered">**if**</span> your script has code that is standalone and independent, we recomend you always start a script by clearing R's brain 
``` rm(list=ls())``` 


<span style="color:orangered">**If**</span>  your script is a function or group of functions to be sourced by another script, skip this step!!

Try typing the ```rm```  function instead of copy pasting it. You will notice Rstudio **closes brackets** for you automatically


##<span style="color:cadetblue">Step 5</span>

Leave another empty "blank line"

##<span style="color:cadetblue">Step 6</span>

###Now you are ready to start writing your first script! Copy paste the code inside the ```[] ``` Then move to <span style="color:cadetblue">Step 7</span>

We will go over how to construct these functions in the next module

A loop

```{r loop}
 for(i in 1:10){ # for loop run from 1 to 10
print("Darwin rules!") # write a sentence 10 times
print(i*i) # also print each number multiplied by itself 
}
```


<span style="color:orangered">Practice:</span> annotate the function

```{r function}

Isit <- function(x){
 if (x == 10)
 print("It's a ten!")
 else print("Not a ten!")
}


Isit(10)

Isit(1)

```

A function and a plot 

```{r plot}

# A simple function that needs functions from the ape library to run
# ape is a library of functions for analysis of evolutionary relationships:
Tree <- function(x){
   #this function creates a plot of a random evolutionary tree
   #of size x
   require(ape)
   tree <- rcoal(x)
   plot(tree)
 }
Tree(30)
```


<span style="color:orangered">**_Check_**:</span> Notice the colours in your script, this is syntax highlighting. Separates:
 
>1. comments
>2. R functions
>3. numbers 
>4. other things


##<span style="color:cadetblue">Step 7</span>

Once you are done writing your script and you are happy with the commenting. <span style="color:orangered">**Save**</span> it in your <span style="color:orangered">**working directory**</span> of your project. Give it a meaningful name.


##<span style="color:cadetblue">Step 8</span>

Open your script and run it!

```
File --> Open file --> Search for your working directory then run all or parts of it
```

<span style="color:orangered">**_Or_**</span> you can double click on your R script open it in R studio and run specific parts of it
``` 
Mac: cmd+return 
Windows: ctrl+enter
or pressing Run 
```


<span style="color:orangered">**_Or_**</span>
```
setwd("your path") # sets your working directory. You can also do this mannually
source("Script1.R") # source your script, rename accordingly
```
##<span style="color:cadetblue">Step 9</span>


It's a good idea to create a README text file that describes your project and keep it in the project
folder. 

This file should describe the overall project and the files in the project folder

###<span style="color:orangered">Practice:</span> Create a README text file

```
File --> New File --> Text file 

Save it using the name README.txt" in the same directory of your project
```